Question: Permission Denied Error While Using Quake
0
gravatar for Medhat
6.2 years ago by
Medhat8.6k
Texas
Medhat8.6k wrote:

I installed Quake following this tutorial Here I installed Jellyfish and boost under /usr/local also R and VGAM package are installed

when I use this command

python quake.py -f /home/medhat/Downloads/genomeList.ls -k 15 -p 2

to use the Quake program it gives me this error

Guessing quality values are on ascii 33 scale
/bin/sh: 1: /home/medhat/source/Quake/bin/jellyfish: Permission denied
/bin/sh: 1: /home/medhat/source/Quake/bin/jellyfish: Permission denied
 Traceback (most recent call last):
 File "quake.py", line 324, in <module>
  main()
 File "quake.py", line 89, in main
  jellyfish(options.readsf, options.reads_listf, options.k, ctsf, quality_scale, options.hash_size, options.proc)
 File "quake.py", line 290, in jellyfish
  os.rename('%s.dbm_0' % output_pre, '%s.dbm' % output_pre)

OSError: [Errno 2] No such file or directory

I used chmod to change permission of the jellyfish director but nothing happened

also I used sudo befor the command "python quake.py -f /home/medhat/Downloads/genomeList.ls -k 15 -p 2" but nothing change lastly the content of the "/home/medhat/Downloads/genomeList.ls" file is path to fastq file /home/medhat/Downloads/frag_1.fastq

Thanks for help

assembly qc • 2.5k views
ADD COMMENTlink modified 6.1 years ago • written 6.2 years ago by Medhat8.6k

You mentioned changing permission on /home/medhat/source/Quake/bin, but have you also checked the permissions on /home/medhat/source/Quake/bin/jellyfish? Specifically, it should be set executable.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Devon Ryan93k

no i did change it sudo chmod -R 777 jellyfish but the same error

ADD REPLYlink written 6.2 years ago by Medhat8.6k
2
gravatar for Medhat
6.1 years ago by
Medhat8.6k
Texas
Medhat8.6k wrote:

OK I manage to make the program run but this is not a solution it just work around I used command "--no_jelly" so it worked till I find the solution . the command will be

python quake.py -f /home/medhat/Downloads/genomeList.ls --no_jelly -k 15 -p 2
ADD COMMENTlink written 6.1 years ago by Medhat8.6k

I have a same problem now, did you find finally any solution how to use jellyfish with quake? because it takes lots of time without it to produce the result.

ADD REPLYlink written 5.0 years ago by mhkt190
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